PROJECT SUMMARY Animal development and differentiation proceeds by the sequential activation of gene expression accompanied by cell division, differential development and movement to form organ primordia. Our primary goal is to elucidate the complex network of spatial and genetic interactions that underlies the processes of normal development, disease and evolution. A comprehensive analysis of these interactions requires knowledge of the gene expression profiles for the complement of protein-coding and non-coding genes in an organism. The Berkeley Drosophila Genome Project (BDGP) has established a gene expression resource for Drosophila embryonic development that contains spatial and temporal expression patterns determined from whole mount RNA in-situ hybridization. These patterns are annotated using a standardized controlled anatomical ontology and the images are presented in a standardized virtual representation of the patterns to facilitate ontology and image based search and analysis. Specifically we propose to produce organ system and gene family RNA expression networks based on spatial patterns of expression and expand the collection to include non-coding genes; assay patterns of expression driven by putative CRMs for transcription factors (TFs) and selected TF target genes and analyze the expression using our computational image analysis tools. The organ system expression profiles produced by our study will provide fundamental information for elucidating embryonic development in Drosophila and, by homology, in other eukaryotes, including humans. The roles of most non- coding RNAs in particular remain unknown. The spatial expression driven by cis-regulatory regions will provide insights into the developmental roles of the transcription factors. The integration of spatiotemporal expression data from coding transcripts, non-coding transcripts and CRM reporters will promote discovery of networks of regulatory interactions. These studies are directed toward the understanding of life processes and lay the foundation for promoting better human health.